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- PDB-3gv4: Crystal structure of human HDAC6 zinc finger domain and ubiquitin... -

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Basic information

Entry
Database: PDB / ID: 3gv4
TitleCrystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG
Components
  • Histone deacetylase 6
  • ubiquitin C-terminal peptide RLRGG
KeywordsHYDROLASE / HDAC6 / zinc finger / ubiquitin C-terminal peptide RLRGG / SGC / Actin-binding / Chromatin regulator / Cytoplasm / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Repressor / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / Cargo trafficking to the periciliary membrane / negative regulation of aggrephagy / response to misfolded protein / positive regulation of protein oligomerization / type 2 mitophagy / negative regulation of protein-containing complex disassembly / peroxidase inhibitor activity ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / Cargo trafficking to the periciliary membrane / negative regulation of aggrephagy / response to misfolded protein / positive regulation of protein oligomerization / type 2 mitophagy / negative regulation of protein-containing complex disassembly / peroxidase inhibitor activity / regulation of autophagy of mitochondrion / tubulin deacetylation / deacetylase activity / Transcriptional regulation by RUNX2 / tubulin deacetylase activity / lysosome localization / cilium disassembly / ATPase inhibitor activity / protein deacetylation / misfolded protein binding / positive regulation of type 2 mitophagy / cytoplasmic ubiquitin ligase complex / regulation of androgen receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / aggresome assembly / Transferases; Acyltransferases; Aminoacyltransferases / aggresome / histone deacetylase activity / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / microtubule associated complex / Notch-HLH transcription pathway / axonal transport of mitochondrion / RUNX2 regulates osteoblast differentiation / regulation of microtubule-based movement / negative regulation of gene expression, epigenetic / histone deacetylase complex / cell leading edge / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of epithelial cell migration / dynein complex binding / cilium assembly / regulation of macroautophagy / HSF1 activation / polyubiquitin modification-dependent protein binding / alpha-tubulin binding / negative regulation of protein-containing complex assembly / beta-tubulin binding / negative regulation of proteolysis / multivesicular body / axon cytoplasm / inclusion body / transcription corepressor binding / regulation of autophagy / ubiquitin binding / regulation of protein stability / Hsp90 protein binding / intracellular protein transport / Late endosomal microautophagy / caveola / beta-catenin binding / protein destabilization / NOTCH1 Intracellular Domain Regulates Transcription / tau protein binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / histone deacetylase binding / Chaperone Mediated Autophagy / Aggrephagy / ubiquitin protein ligase activity / cellular response to heat / actin binding / microtubule binding / microtubule / perikaryon / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / dendrite / perinuclear region of cytoplasm / enzyme binding / DNA-templated transcription / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein deacetylase HDAC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsDong, A. / Ravichandran, M. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. ...Dong, A. / Ravichandran, M. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Dhe-Paganon, S. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG
Authors: Dong, A. / Ravichandran, M. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Dhe-Paganon, S. / Min, J. / Ouyang, H.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase 6
H: ubiquitin C-terminal peptide RLRGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8206
Polymers12,5832
Non-polymers2364
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-6 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.657, 36.093, 88.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone deacetylase 6 / HD6


Mass: 12023.739 Da / Num. of mol.: 1 / Fragment: UNP residues 1109-1215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6, KIAA0901, JM21 / Plasmid: P28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBN7, histone deacetylase
#2: Protein/peptide ubiquitin C-terminal peptide RLRGG


Mass: 559.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ubiquitin C-terminal peptide
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 14, 2008 / Details: VariMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 10865 / Num. obs: 10865 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 14.1
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 4.26 / Num. unique all: 813 / Rsym value: 0.231 / % possible all: 72.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASESphasing
REFMAC5.2.0019refinement
Coot0.3.3model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C5K

3c5k


Resolution: 1.72→33.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.51 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.125 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23034 609 5.6 %RANDOM
Rwork0.17382 ---
all0.17695 10213 --
obs0.17695 10213 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.958 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---1.31 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.72→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms799 0 4 205 1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9211128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52723.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32215116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.224152
X-RAY DIFFRACTIONr_chiral_restr0.0930.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02640
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2438
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2551
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.5520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.022821
X-RAY DIFFRACTIONr_scbond_it1.5953355
X-RAY DIFFRACTIONr_scangle_it2.474.5307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.762 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 34 -
Rwork0.378 523 -
obs--67.68 %

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